NavList:

Thanks DaveP. 
Yes, I was clear of Indented Head and had a sea horizon to use under Flinders Peak. It is called Station Peak in some sources. The small collection of hills is called the You Yangs.

As an aside, Matthew Flinders climbed to the top of the range, hence Flinders Peak, when exploring Port Phillip around 1802. As a navigator and surveyor, Flinders must rank among the greatest. Together with Cook and Bligh, their charting accomplishments in this part of the world were superb. The French were here at the same time also exploring. French navigator Nicholas Baudin circumnavigated Australia clockwise while Flinders was going around anti clockwise. They met off the coast of South Australia and shared a courteous dinner. Flinders named that meeting place Encounter Bay. Many places in Tasmania have French names as part of Baudin's work was retained. But Baudin's ship was a sickly one and many crew were lost through disease. Ultimately his efforts to gain the upper hand over the English failed. 

As a further aside, Margaret Cameron-Ash has written a detailed account of what she believes explains why Cook, sailing up the east coast in 1770, found Botany Bay but did not find Port Jackson (ie Sydney harbour.) which is just around the next headland. Her theory is set out in her book Lying for the Admiralty. Spolier alert: he didn't fail to notice Port Jackson. He found it and recognised its strategic worth but kept that knowledge secret until he could get back to the Admiralty. Worth reading.

Back to Port Phillip, perhaps the bigger hill further north you refer to is Mt Macedon. It is visible from a good part of Port Phillip but its peak is not as clearly defined as it is for Flinders. Macedon is a bit flat topped. Arthur's Seat in the SE is also a possibility and it is conveniently close to shore. I'll keep practicing. I am also curious to find out what is going on with my compass bearings. Besides making an error on Flinders, I also took a transit on passing Fawkner Beacon with a high tower a little way inland to the east and read about 10 deg off the true bearing. Variation here is 12 deg east. I need to investigate.